RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10177
(116 letters)
>1i8f_A Putative snRNP SM-like protein; beta barrel-like SMAP monomers
form 35-stranded beta-sheet I heptamer, structural
genomics; 1.75A {Pyrobaculum aerophilum} SCOP: b.38.1.1
PDB: 1lnx_A*
Length = 81
Score = 67.8 bits (166), Expect = 1e-16
Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
+V LRD + G LRS DQ NL+L E I GN Y RG ++RGENV+ + V
Sbjct: 25 LVKLRDSHEIRGILRSFDQHVNLLLEDAEEIID-GNVY---KRGTMVVRGENVLFISPVP 80
>3bw1_A SMX4 protein, U6 snRNA-associated SM-like protein LSM3;
RNA-binding protein, SM protein, ring, HOMO octamer,
mRNA processing; 2.50A {Saccharomyces cerevisiae}
Length = 96
Score = 65.1 bits (159), Expect = 2e-15
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 4/68 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYG----DIPRGIFIIRGENVVLM 56
+ LR RTL+G L++ D N+VL +E I+ N + + IRG+ V L+
Sbjct: 24 YIKLRGARTLVGTLQAFDSHCNIVLSDAVETIYQLNNEELSESERRCEMVFIRGDTVTLI 83
Query: 57 GEVDKEKE 64
++ +
Sbjct: 84 STPSEDDD 91
>3s6n_G Small nuclear ribonucleoprotein G; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_G 2y9c_G 2y9d_G 3cw1_G 3pgw_G* 2y9a_G
Length = 76
Score = 63.5 bits (155), Expect = 5e-15
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
+ L GR + G LR D F NLV+ + +E G Q G+ +IRG +++++ ++
Sbjct: 18 SLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQ---NNIGMVVIRGNSIIMLEALE 74
Query: 61 K 61
+
Sbjct: 75 R 75
>4emk_C U6 snRNA-associated SM-like protein LSM7; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_C
Length = 113
Score = 64.2 bits (156), Expect = 8e-15
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGD----IPRGIFIIRGENVVLM 56
GR + G L+ DQ NLVL E++ G+ ++RG +VL+
Sbjct: 37 QATFTGGRQITGILKGFDQLMNLVLDDVEEQLRNPEDGKLTGAIRKLGLVVVRGTTLVLI 96
Query: 57 GEVDKEKE 64
+D +E
Sbjct: 97 APMDGSEE 104
>1d3b_B Protein (small nuclear ribonucleoprotein associat B); snRNP,
splicing, core snRNP domain, systemic lupus eryth SLE,
RNA binding protein; HET: CIT; 2.00A {Homo sapiens}
SCOP: b.38.1.1 PDB: 2y9a_A 2y9b_A 2y9c_A 2y9d_A
Length = 91
Score = 58.7 bits (142), Expect = 6e-13
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR-------GIFIIRGENVV 54
+L+DGR IG ++ D+ NL+L E + + G+ ++RGEN+V
Sbjct: 19 CILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV 78
Query: 55 LMGEVD 60
M V+
Sbjct: 79 SM-TVE 83
>1th7_A SnRNP-2, small nuclear riboprotein protein; archaea, SM protein,
SM fold, SS-SM1, RNA binding protein; 1.68A {Sulfolobus
solfataricus} SCOP: b.38.1.1
Length = 81
Score = 55.8 bits (135), Expect = 6e-12
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 7/62 (11%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVG--NQYGDIPRGIFIIRGENVVLMGE 58
+V L+ + + G LRS DQ NLVL + E G + G I +IRG+NV+L+
Sbjct: 23 LVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQSDGSGKKLGTI-----VIRGDNVILISP 77
Query: 59 VD 60
+
Sbjct: 78 LQ 79
>3s6n_F Small nuclear ribonucleoprotein F; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_F 2y9c_F 2y9d_F 3cw1_F 3pgw_F* 2y9a_F
Length = 86
Score = 51.7 bits (124), Expect = 3e-10
Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
MV L+ G GYL SVD + N+ L T E I G G + G +IR NV+ + V+
Sbjct: 20 MVKLKWGMEYKGYLVSVDGYMNMQLANTEEYID-GALSGHL--GEVLIRCNNVLYIRGVE 76
Query: 61 KEKE 64
+E+E
Sbjct: 77 EEEE 80
>4emk_B U6 snRNA-associated SM-like protein LSM6; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_B
Length = 75
Score = 50.4 bits (121), Expect = 7e-10
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
++ L G G L +D + NL L +T E ++ G + G IRG NV+ + +D
Sbjct: 18 LIRLSSGVDYKGILSCLDGYMNLALERTEEYVN-GKKTNVY--GDAFIRGNNVLYVSALD 74
>1i4k_A Putative snRNP SM-like protein; core snRNP domain, RNA binding
protein; HET: CIT; 2.50A {Archaeoglobus fulgidus} SCOP:
b.38.1.1 PDB: 1i5l_A*
Length = 77
Score = 49.2 bits (118), Expect = 2e-09
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 7/63 (11%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLMGE 58
+V L+ GR G L D NLVL E + V + G + +IRG+ VV +
Sbjct: 18 IVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQNGEVVRKVGSV-----VIRGDTVVFVSP 72
Query: 59 VDK 61
Sbjct: 73 APG 75
>4emg_A Probable U6 snRNA-associated SM-like protein LSM3; SM fold, mRNA
decay, LSM proteins, RNA binding protein; 2.70A
{Schizosaccharomyces pombe}
Length = 93
Score = 47.9 bits (114), Expect = 9e-09
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR----------GIFIIRG 50
V LR R L G L + D+ N+VL E + + + + +RG
Sbjct: 23 YVKLRGDRELNGRLHAYDEHLNMVLGDAEEIVTIFDDEETDKDKALKTIRKHYEMLFVRG 82
Query: 51 ENVVLM 56
++V+L+
Sbjct: 83 DSVILI 88
>1mgq_A SM-like protein; LSM, RNA-binding, archea, RNA binding protein;
1.70A {Methanothermobacterthermautotrophicus} SCOP:
b.38.1.1 PDB: 1i81_A 1loj_A* 1jbm_A 1jri_A
Length = 83
Score = 47.7 bits (114), Expect = 1e-08
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLM 56
++ L+ R G L+S D NLVL+ E V + G + +IRG+N+V +
Sbjct: 29 IIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTV-----LIRGDNIVYI 81
>1h64_1 SnRNP SM-like protein; SM fold, spliceosome, snRNP core; 1.9A
{Pyrococcus abyssi} SCOP: b.38.1.1 PDB: 1m8v_A*
Length = 75
Score = 46.9 bits (112), Expect = 2e-08
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERI--HVGNQYGDIPRGIFIIRGENVVLMGE 58
+V+L+ G G L D N+VL V +YG I +IRG+NV+ +
Sbjct: 18 LVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKI-----VIRGDNVLAISP 72
Query: 59 VDK 61
++
Sbjct: 73 TEE 75
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_A
Length = 231
Score = 47.7 bits (113), Expect = 7e-08
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIE-RIHVGNQYGDIPR------GIFIIRGENVV 54
+L+DGR IG ++ D+ NL+L E R R G+ ++RGEN+V
Sbjct: 19 CILQDGRIFIGTFKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGLVLLRGENLV 78
>2fwk_A U6 snRNA-associated SM-like protein LSM5; structural genomics,
structural genomics consortium, SGC, DNA binding
protein; 2.14A {Cryptosporidium parvum} SCOP: b.38.1.1
PDB: 3pgg_A
Length = 121
Score = 44.6 bits (105), Expect = 3e-07
Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 12/67 (17%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR------------GIFIIR 49
V+++ + G LR D++ N+VL E ++ ++
Sbjct: 43 VVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFKADEEDISGGNKKLKRVMVNRLETILLS 102
Query: 50 GENVVLM 56
G NV ++
Sbjct: 103 GNNVAML 109
>1n9r_A SMF, small nuclear ribonucleoprotein F, snRNP-F, SM protein F;
heptamer, translation; 2.80A {Saccharomyces cerevisiae}
SCOP: b.38.1.1 PDB: 1n9s_A
Length = 93
Score = 41.7 bits (98), Expect = 3e-06
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 3 LLRDGRTLIGYLRSVDQFANLVLHKTIERIH--VGNQYGDIPRGIFIIRGENVVLMGEVD 60
L + G L S D + NL L++ E + G+I IR NV+ + E+
Sbjct: 38 LKFNSTEYRGTLVSTDNYFNLQLNEAEEFVAGVSHGTLGEI-----FIRCNNVLYIRELP 92
>1ljo_A Archaeal SM-like protein AF-SM2; snRNP, core snRNP domain, RNA
binding protein, unknown F; 1.95A {Archaeoglobus
fulgidus} SCOP: b.38.1.1
Length = 77
Score = 40.8 bits (96), Expect = 4e-06
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 1 MVLLRDGRTLI-GYLRSVDQFANLVLHKTIERIHVG--NQYGDIPRGIFIIRGENVVLMG 57
V ++ + G L VD + NL L +E G+I ++RG NVVL+
Sbjct: 19 RVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEI-----VLRGNNVVLIQ 73
Query: 58 EVDK 61
++
Sbjct: 74 PQEE 77
>4emk_A U6 snRNA-associated SM-like protein LSM5; SM fold, mRNA decay and
PRE-mRNA splicing, LSM proteins, RNA protein; 2.30A
{Schizosaccharomyces pombe} PDB: 3swn_A
Length = 94
Score = 39.8 bits (93), Expect = 1e-05
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56
V+++ R G L D + N+VL E V ++ G + ++
Sbjct: 35 VIMKSEREFAGTLVGFDDYVNIVLKDVTEYDTVTGVTEKHSE--MLLNGNGMCML 87
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 38.9 bits (90), Expect = 1e-04
Identities = 31/140 (22%), Positives = 52/140 (37%), Gaps = 37/140 (26%)
Query: 11 IGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGEN-VVLMGEVDKEKEHCPQL 69
IG +R + + N L +I + N G +P + I + V+K H P
Sbjct: 306 IG-VRCYEAYPNTSLPPSILEDSLENNEG-VPSPMLSISNLTQEQVQDYVNKTNSHLPAG 363
Query: 70 QQVSV---------------EDI--LNAQ-RKEQ-EVKQERSRM-LAKRLKERGLSFVP- 108
+QV + + + LN RK + ++SR+ ++R + F+P
Sbjct: 364 KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423
Query: 109 -------------DLINDDL 115
DLIN DL
Sbjct: 424 ASPFHSHLLVPASDLINKDL 443
Score = 27.3 bits (60), Expect = 1.3
Identities = 27/124 (21%), Positives = 37/124 (29%), Gaps = 56/124 (45%)
Query: 33 HVGNQYG----DI----PRGIFI---------IRGENVVLM-------GEVDKEK----- 63
H + YG DI P + I IR EN M G++ EK
Sbjct: 1652 HFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR-ENYSAMIFETIVDGKLKTEKIFKEI 1710
Query: 64 -EHCPQLQQVSVEDIL----NAQRKEQEVKQERSRMLA------KRLKERGLSFVPDLIN 112
EH S + +L Q + + LK +GL +P
Sbjct: 1711 NEHSTSYTFRSEKGLLSATQFTQP----------ALTLMEKAAFEDLKSKGL--IPA--- 1755
Query: 113 DDLF 116
D F
Sbjct: 1756 DATF 1759
>4emh_A Probable U6 snRNA-associated SM-like protein LSM4; SM fold, mRNA
decay, PRE-mRNA splicing, LSM proteins, RNA BI protein;
2.20A {Schizosaccharomyces pombe}
Length = 105
Score = 36.6 bits (85), Expect = 3e-04
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 17/90 (18%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
+V L++G T G+L + D + NL L + I + G+++ +P + IRG N+ +
Sbjct: 30 LVELKNGETFNGHLENCDNYMNLTLREVIRTMPDGDKFFRLPE-CY-IRGNNIKYL---- 83
Query: 61 KEKEHCPQLQQVSVEDILNAQRKEQEVKQE 90
+++L+ K+Q ++E
Sbjct: 84 ----RIQ-------DEVLSQVAKQQAQQRE 102
>3s6n_E Small nuclear ribonucleoprotein E; SMN complex, SMN-gemin2
complex, U-rich snRNA, SM fold, SM C SNRNPS, snRNP
biogenesis, PRE-mRNA splicing; 2.50A {Homo sapiens}
PDB: 2y9b_E 2y9c_E 2y9d_E 3cw1_E 3pgw_E* 2y9a_E
Length = 92
Score = 33.6 bits (77), Expect = 0.002
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
+ + + G + D++ NLVL E G +++G+N+ L+ V
Sbjct: 34 WLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTK--SRKQLGRIMLKGDNITLLQSVS 91
>1b34_B Protein (small nuclear ribonucleoprotein SM D2); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_C 2y9b_C 2y9c_C 2y9d_C 3cw1_C 3pgw_Y*
3s6n_B
Length = 118
Score = 34.2 bits (78), Expect = 0.003
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 11/66 (16%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIF-----------IIR 49
++ R+ + L+G +++ D+ N+VL E + G + +R
Sbjct: 43 LINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLR 102
Query: 50 GENVVL 55
G++V++
Sbjct: 103 GDSVIV 108
>2y9a_D Small nuclear ribonucleoprotein SM D3; splicing-RNA complex,
PRE-mRNA splicing, spliceosome, snRNP biogenesis, SM
site, SM fold, heteromeric heptameric ring; 3.60A {Homo
sapiens} PDB: 2y9b_D 2y9c_D 2y9d_D 3pgw_Z* 3cw1_D
Length = 126
Score = 33.5 bits (76), Expect = 0.006
Identities = 12/103 (11%), Positives = 27/103 (26%), Gaps = 10/103 (9%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVD 60
G G L + N + G IRG + +
Sbjct: 19 TCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRV---AQLEQVYIRGSKIRFL---- 71
Query: 61 KEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERG 103
L+ + + + + + ++ +L ++ RG
Sbjct: 72 ---ILPDMLKNAPMLKSMKNKNQGSGAGRGKAAILKAQVAARG 111
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.0 bits (74), Expect = 0.011
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 14/35 (40%)
Query: 83 KEQEVKQERSRMLAKRLKERGLSFVPD----L-IN 112
++Q +K+ L LK L + D L I
Sbjct: 18 EKQALKK-----LQASLK---L-YADDSAPALAIK 43
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 32.1 bits (72), Expect = 0.027
Identities = 19/120 (15%), Positives = 36/120 (30%), Gaps = 36/120 (30%)
Query: 3 LLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIF----IIRGENV----- 53
+RDG + V+ L IE + R +F + +
Sbjct: 336 SIRDGLATWDNWKHVNCDK---LTTIIESS-LNVLEPAEYRKMFDRLSVFP-PSAHIPTI 390
Query: 54 VLM---GEVDKEKEHCPQLQQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDL 110
+L +V K V ++N K + ++ K+ KE +P +
Sbjct: 391 LLSLIWFDVIKS----------DVMVVVN--------KLHKYSLVEKQPKE-STISIPSI 431
Score = 27.9 bits (61), Expect = 0.87
Identities = 19/111 (17%), Positives = 31/111 (27%), Gaps = 13/111 (11%)
Query: 13 YLRSVDQFANLVLH-----KTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCP 67
+ D +N+ L + R+ Y + ++ NV + C
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPY---ENCLLVLL--NVQNAKAWNAFNLSCK 267
Query: 68 QL---QQVSVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVPDLINDDL 115
L + V D L+A S L + L D DL
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing,
core snRNP domain, systemic lupus eryth SLE, RNA
binding protein; HET: CIT; 2.00A {Homo sapiens} SCOP:
b.38.1.1
Length = 75
Score = 29.7 bits (67), Expect = 0.053
Identities = 9/56 (16%), Positives = 13/56 (23%), Gaps = 7/56 (12%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGN--QYGDIPRGIFIIRGENVV 54
G G L + N + G Q + IRG +
Sbjct: 19 TCETNTGEVYRGKLIEAEDNMNCQMSNITVTYRDGRVAQLEQV-----YIRGCKIR 69
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing,
spliceosome, core snRNP domain, systemi erythematosus,
SLE, RNA binding protein; 2.50A {Homo sapiens} SCOP:
b.38.1.1 PDB: 2y9a_B 2y9b_B 2y9c_B 2y9d_B 3cw1_B 3pgw_X*
3s6n_A
Length = 119
Score = 30.3 bits (68), Expect = 0.057
Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 7/101 (6%)
Query: 4 LRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEK 63
L++G + G + VD N L + + IRG N+ +
Sbjct: 19 LKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREP---VQLETLSIRGNNIRYF-ILPDSL 74
Query: 64 EHCPQLQQVSVEDILNAQRKEQEVKQERSR-MLAKRLKERG 103
L V + ++++E + R R R + RG
Sbjct: 75 PLDTLLVDVEPKV--KSKKREAVAGRGRGRGRGRGRGRGRG 113
>1zpu_A Iron transport multicopper oxidase FET3; ferroxidase, oxidoreduc;
HET: NAG BMA MAN NDG; 2.80A {Saccharomyces cerevisiae}
Length = 534
Score = 31.1 bits (71), Expect = 0.061
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 9/35 (25%)
Query: 33 HVGNQYGDIPRGIFIIRG---------ENVVLMGE 58
H QY D +G+FII+ E + + E
Sbjct: 107 HTDGQYEDGMKGLFIIKDDSFPYDYDEELSLSLSE 141
>2q9o_A Laccase-1; multicopper oxidase, 2-OXOH oxidoreductase; HET: OHI NAG
MAN GOL; 1.30A {Melanocarpus albomyces} SCOP: b.6.1.3
b.6.1.3 b.6.1.3 PDB: 3fu7_A* 3fu8_A* 3fu7_B* 1gw0_A*
2ih9_A* 2ih8_A* 3fu9_A* 3qpk_A* 3dkh_A* 3pps_A*
Length = 559
Score = 29.2 bits (66), Expect = 0.27
Identities = 8/35 (22%), Positives = 11/35 (31%), Gaps = 9/35 (25%)
Query: 33 HVGNQYGDIPRGIFIIRG---------ENVVLMGE 58
H QYG+ G I G V + +
Sbjct: 140 HFSAQYGNGVVGTIQINGPASLPYDIDLGVFPITD 174
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 29.1 bits (65), Expect = 0.28
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 6/92 (6%)
Query: 5 RDGRTLIGYLRS------VDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58
R+ L+ LR+ ++ +++ + + + G + R +FI+ + + E
Sbjct: 591 RNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKE 650
Query: 59 VDKEKEHCPQLQQVSVEDILNAQRKEQEVKQE 90
+ K H +L +DI +E
Sbjct: 651 LKVRKGHIAKLMATEYQDIEGGFEDVEEYTWS 682
>2jg6_A DNA-3-methyladenine glycosidase; 3-methyladenine-DNA-glycosylase-I,
hydrolase; 1.70A {Staphylococcus aureus} PDB: 4aia_A*
4ai5_A* 4ai4_A
Length = 186
Score = 28.6 bits (65), Expect = 0.30
Identities = 6/33 (18%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 77 ILNAQRKEQEV--KQERSRMLAKRLKERGLSFV 107
+ + + L+K LK+ G F+
Sbjct: 125 KDLQYEHASDRITVDDTATQLSKDLKQYGFKFL 157
>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base
excision, helix-hairpin-helix, hydrolase; HET: PGE;
1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A
1p7m_A*
Length = 183
Score = 28.6 bits (65), Expect = 0.35
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 77 ILNAQRKEQEV--KQERSRMLAKRLKERGLSFV 107
+ ++ S LAK LK+RG FV
Sbjct: 125 QITQAASLDKIPTSTPASDALAKALKKRGFKFV 157
>3sqr_A Laccase; multicopper oxidase, glycosylation, oxidoreductase; HET:
NAG BMA MAN; 1.67A {Botrytis aclada}
Length = 580
Score = 27.4 bits (61), Expect = 1.2
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 33 HVGNQYGDIPRGIFIIRG 50
H QYGD G II G
Sbjct: 170 HFSLQYGDGLFGPLIING 187
>3pxl_A Laccase; 4-copper protein, metal-binding, oxidoreductase, type-2
Cu-D; HET: NAG BMA MAN; 1.20A {Trametes hirsuta} PDB:
3fpx_A* 3v9c_A* 3div_A* 2h5u_A* 2xyb_A* 1kya_A* 1gyc_A*
2qt6_A* 2hrg_A* 2hrh_A* 4a2f_A* 2vdz_A* 4a2d_A* 4a2e_A*
4a2g_A* 4a2h_A* 2ve0_A* 2vds_A* 2hzh_A* 3kw7_A*
Length = 499
Score = 26.9 bits (60), Expect = 1.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 33 HVGNQYGDIPRGIFIIRGEN 52
H+ QY D RG F++ N
Sbjct: 111 HLSTQYCDGLRGPFVVYDPN 130
>3t6v_A Laccase; beta barrel, oxidoreductase; HET: CBS; 2.00A {Steccherinum
ochraceum} PDB: 3t6w_A* 3t6x_A* 3t6z_A* 3t71_A*
Length = 495
Score = 26.9 bits (60), Expect = 1.9
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 33 HVGNQYGDIPRGIFIIRG 50
H+ QY D RG F++
Sbjct: 112 HLTTQYCDGLRGPFVVYD 129
>3t18_A Aminotransferase class I and II; PSI-biology, MCSG, midwest center
for structural genomics, P 5'-phosphate binding; HET:
PLP; 2.86A {Anaerococcus prevotii}
Length = 413
Score = 26.9 bits (60), Expect = 1.9
Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 10/46 (21%)
Query: 74 VEDILN--AQRKE--QEVKQERSRM------LAKRLKERGLSFVPD 109
+ L +K QE+ R+ + KE L+ +P
Sbjct: 308 ILIELERAENKKIYEQELVDLRNMLKSRADVFVTAAKENKLTMIPY 353
>3g7q_A Valine-pyruvate aminotransferase; NP_462565.1, structur genomics,
joint center for structural genomics, JCSG, prote
structure initiative; HET: MSE; 1.80A {Salmonella
typhimurium}
Length = 417
Score = 26.5 bits (59), Expect = 2.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 92 SRMLAKRLKERGLSFVP 108
+ +L +RLK RG+ VP
Sbjct: 353 TELLYQRLKARGVLMVP 369
>1hfu_A Laccase 1; oxidoreductase, blue multi-copper oxidase, type-2 copper
depleted, signal, glycoprotein; HET: MAN NAG NDG; 1.68A
{Coprinus cinereus} SCOP: b.6.1.3 b.6.1.3 b.6.1.3 PDB:
1a65_A*
Length = 503
Score = 26.5 bits (59), Expect = 2.6
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 33 HVGNQYGDIPRGIFIIRGEN 52
H G QY D RG +I +N
Sbjct: 111 HFGTQYCDGLRGPMVIYDDN 130
>1v10_A Laccase; multicopper blue oxidase, oxidase; 1.7A {Rigidoporus
lignosus} SCOP: b.6.1.3 b.6.1.3 b.6.1.3
Length = 521
Score = 25.7 bits (57), Expect = 4.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 33 HVGNQYGDIPRGIFIIRGEN 52
H+ QY D RG F++ N
Sbjct: 132 HLSTQYCDGLRGAFVVYDPN 151
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.1 bits (54), Expect = 5.4
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 81 QRKEQEVKQERSRMLAKRLKERG 103
QRK + S+++ + +E+
Sbjct: 94 QRKRLQELDAASKVMEQEWREKA 116
>1gsa_A Glutathione synthetase; ligase; HET: ADP GSH; 2.00A {Escherichia
coli} SCOP: c.30.1.3 d.142.1.1 PDB: 1gsh_A 2glt_A 1glv_A
Length = 316
Score = 24.9 bits (55), Expect = 8.2
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 89 QERSRMLAKRLKERGLSFV-PDLINDDL 115
+ +R + LKE+GL FV D+I D L
Sbjct: 252 WKIARQIGPTLKEKGLIFVGLDIIGDRL 279
>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A
3kso_A 3kss_A
Length = 1054
Score = 24.8 bits (55), Expect = 9.9
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 11 IGYLRSVDQFANLVLHKTIER--IHVGN----QYGDIPR-GIFIIRGEN-----VVLM 56
GYL+++D F ++VL + +++ + Q G R GI + GE VV++
Sbjct: 241 SGYLQTLDDFNHIVLKASENGVPVYLRDVAKVQIGPEMRRGIAELNGEGEVAGGVVIL 298
>3if2_A Aminotransferase; YP_265399.1, structura genomics, joint center for
structural genomics, JCSG, prote structure initiative,
PSI-2; HET: PLP; 2.50A {Psychrobacter arcticus 273-4}
Length = 444
Score = 24.7 bits (54), Expect = 9.9
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 92 SRMLAKRLKERGLSFVP 108
+ L +RLK +G VP
Sbjct: 379 TLDLYERLKAKGTLIVP 395
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.142 0.397
Gapped
Lambda K H
0.267 0.0581 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,761,955
Number of extensions: 98320
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 68
Length of query: 116
Length of database: 6,701,793
Length adjustment: 79
Effective length of query: 37
Effective length of database: 4,496,034
Effective search space: 166353258
Effective search space used: 166353258
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.7 bits)